Starting phenix.real_space_refine on Mon Sep 14 02:57:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6mzb_9297/09_2026/6mzb_9297_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6mzb_9297/09_2026/6mzb_9297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6mzb_9297/09_2026/6mzb_9297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6mzb_9297/09_2026/6mzb_9297.map" model { file = "/net/cci-nas-00/data/ceres_data/6mzb_9297/09_2026/6mzb_9297_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6mzb_9297/09_2026/6mzb_9297_trim.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.157 sd= 1.341 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2 5.49 5 Mg 2 5.21 5 S 97 5.16 5 C 8991 2.51 5 N 2367 2.21 5 O 2605 1.98 5 H 13839 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27905 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 12982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 807, 12982 Classifications: {'peptide': 807} Link IDs: {'PTRANS': 31, 'TRANS': 775} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 13314 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 820, 13306 Classifications: {'peptide': 820} Link IDs: {'PTRANS': 31, 'TRANS': 788} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 820, 13306 Classifications: {'peptide': 820} Link IDs: {'PTRANS': 31, 'TRANS': 788} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 13450 Chain: "C" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 796 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 4, 'TRANS': 43} Chain breaks: 1 Chain: "D" Number of atoms: 763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 763 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 4, 'TRANS': 41} Chain breaks: 1 Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Unusual residues: {' MG': 1, ' ZN': 1, '35G%rna3p': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Unusual residues: {' MG': 1, ' ZN': 1, '35G%rna3p': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLY A 345 " occ=0.50 ... (12 atoms not shown) pdb=" HA3BGLY A 345 " occ=0.50 Time building chain proxies: 5.60, per 1000 atoms: 0.20 Number of scatterers: 27905 At special positions: 0 Unit cell: (165.048, 122.728, 119.554, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 S 97 16.00 P 2 15.00 Mg 2 11.99 O 2605 8.00 N 2367 7.00 C 8991 6.00 H 13839 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 92 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 951.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 563 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 599 " pdb=" ZN B 901 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 561 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 597 " 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3288 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 5 sheets defined 56.3% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'B' and resid 47 through 66 removed outlier: 3.713A pdb=" N GLN B 52 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL B 53 " --> pdb=" O GLU B 49 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 88 removed outlier: 3.593A pdb=" N LYS B 78 " --> pdb=" O ARG B 74 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG B 82 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER B 85 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 123 removed outlier: 3.807A pdb=" N CYS B 122 " --> pdb=" O VAL B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 129 removed outlier: 4.022A pdb=" N GLU B 129 " --> pdb=" O PRO B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.679A pdb=" N ALA B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 167 removed outlier: 4.219A pdb=" N LEU B 167 " --> pdb=" O PHE B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 213 removed outlier: 3.955A pdb=" N GLU B 206 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL B 208 " --> pdb=" O GLU B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 247 removed outlier: 3.842A pdb=" N LEU B 220 " --> pdb=" O GLY B 216 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE B 247 " --> pdb=" O ALA B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 264 removed outlier: 3.955A pdb=" N VAL B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 344 through 351 removed outlier: 3.562A pdb=" N ALA B 349 " --> pdb=" O PRO B 345 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU B 350 " --> pdb=" O THR B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 428 Processing helix chain 'B' and resid 429 through 457 Processing helix chain 'B' and resid 459 through 466 removed outlier: 4.537A pdb=" N GLN B 464 " --> pdb=" O GLU B 461 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU B 465 " --> pdb=" O GLU B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 473 removed outlier: 3.864A pdb=" N ARG B 472 " --> pdb=" O PRO B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 493 removed outlier: 3.758A pdb=" N LYS B 487 " --> pdb=" O ASP B 483 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE B 488 " --> pdb=" O GLU B 484 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU B 491 " --> pdb=" O LYS B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 527 removed outlier: 3.892A pdb=" N VAL B 517 " --> pdb=" O GLU B 513 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS B 518 " --> pdb=" O LEU B 514 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU B 527 " --> pdb=" O MET B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 551 removed outlier: 3.691A pdb=" N TYR B 551 " --> pdb=" O VAL B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 576 Processing helix chain 'B' and resid 583 through 596 removed outlier: 3.871A pdb=" N MET B 590 " --> pdb=" O GLU B 586 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR B 592 " --> pdb=" O PHE B 588 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 593 " --> pdb=" O ALA B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 613 removed outlier: 3.784A pdb=" N GLN B 609 " --> pdb=" O ASN B 605 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET B 610 " --> pdb=" O ASN B 606 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS B 611 " --> pdb=" O LEU B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 620 removed outlier: 3.564A pdb=" N LYS B 618 " --> pdb=" O ASN B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 637 removed outlier: 3.773A pdb=" N LEU B 630 " --> pdb=" O GLU B 626 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU B 631 " --> pdb=" O ARG B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 667 removed outlier: 4.147A pdb=" N ILE B 665 " --> pdb=" O ASP B 661 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA B 666 " --> pdb=" O ILE B 662 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 667 " --> pdb=" O ALA B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 675 removed outlier: 3.627A pdb=" N LYS B 674 " --> pdb=" O ALA B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 686 Processing helix chain 'B' and resid 691 through 700 removed outlier: 3.586A pdb=" N VAL B 696 " --> pdb=" O ARG B 692 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU B 697 " --> pdb=" O LYS B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 719 removed outlier: 3.868A pdb=" N LYS B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B 715 " --> pdb=" O ALA B 711 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS B 717 " --> pdb=" O MET B 713 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP B 718 " --> pdb=" O MET B 714 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 719 " --> pdb=" O THR B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 751 removed outlier: 3.782A pdb=" N LYS B 731 " --> pdb=" O GLU B 727 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR B 749 " --> pdb=" O ASP B 745 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL B 750 " --> pdb=" O LEU B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 764 removed outlier: 5.985A pdb=" N ARG B 761 " --> pdb=" O MET B 758 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ASN B 762 " --> pdb=" O MET B 759 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 764 " --> pdb=" O ARG B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 766 through 778 removed outlier: 3.953A pdb=" N LEU B 770 " --> pdb=" O GLU B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 781 through 790 removed outlier: 3.901A pdb=" N SER B 787 " --> pdb=" O TYR B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 823 removed outlier: 4.235A pdb=" N PHE B 797 " --> pdb=" O ILE B 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 16 Processing helix chain 'A' and resid 20 through 35 removed outlier: 3.909A pdb=" N LEU A 26 " --> pdb=" O GLN A 22 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ALA A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LYS A 31 " --> pdb=" O ARG A 27 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 66 removed outlier: 3.904A pdb=" N GLU A 59 " --> pdb=" O VAL A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 89 removed outlier: 3.602A pdb=" N PHE A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 124 Processing helix chain 'A' and resid 138 through 148 removed outlier: 3.857A pdb=" N GLY A 142 " --> pdb=" O MET A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 164 through 170 removed outlier: 3.828A pdb=" N THR A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 169 " --> pdb=" O PHE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 215 removed outlier: 3.786A pdb=" N GLU A 208 " --> pdb=" O THR A 204 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU A 209 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 220 removed outlier: 3.502A pdb=" N LEU A 220 " --> pdb=" O ASN A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 250 removed outlier: 3.744A pdb=" N PHE A 225 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS A 247 " --> pdb=" O TRP A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 266 removed outlier: 3.800A pdb=" N VAL A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 290 Processing helix chain 'A' and resid 291 through 297 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 413 through 430 removed outlier: 3.788A pdb=" N LEU A 419 " --> pdb=" O MET A 415 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET A 420 " --> pdb=" O ASP A 416 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 422 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 458 removed outlier: 3.614A pdb=" N GLU A 438 " --> pdb=" O PRO A 434 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN A 441 " --> pdb=" O TYR A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 466 removed outlier: 4.146A pdb=" N GLN A 466 " --> pdb=" O ASN A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 482 Processing helix chain 'A' and resid 483 through 493 removed outlier: 4.492A pdb=" N GLU A 489 " --> pdb=" O GLU A 485 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ILE A 490 " --> pdb=" O GLU A 486 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY A 493 " --> pdb=" O GLU A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 502 Processing helix chain 'A' and resid 514 through 529 removed outlier: 3.622A pdb=" N LEU A 518 " --> pdb=" O THR A 514 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL A 519 " --> pdb=" O GLU A 515 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR A 526 " --> pdb=" O GLY A 522 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 529 " --> pdb=" O MET A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 536 Processing helix chain 'A' and resid 538 through 553 removed outlier: 3.606A pdb=" N SER A 550 " --> pdb=" O MET A 546 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 551 " --> pdb=" O TYR A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 577 removed outlier: 3.503A pdb=" N GLY A 564 " --> pdb=" O ASN A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 598 removed outlier: 3.644A pdb=" N THR A 594 " --> pdb=" O LEU A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 615 Processing helix chain 'A' and resid 616 through 622 removed outlier: 3.525A pdb=" N LEU A 621 " --> pdb=" O PRO A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 640 removed outlier: 3.559A pdb=" N LYS A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR A 637 " --> pdb=" O GLU A 633 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 638 " --> pdb=" O PHE A 634 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 639 " --> pdb=" O GLY A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 669 removed outlier: 3.602A pdb=" N HIS A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP A 663 " --> pdb=" O ILE A 659 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE A 664 " --> pdb=" O HIS A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 677 removed outlier: 3.743A pdb=" N LYS A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 689 removed outlier: 3.982A pdb=" N LYS A 683 " --> pdb=" O THR A 679 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE A 684 " --> pdb=" O MET A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 705 removed outlier: 4.420A pdb=" N TYR A 700 " --> pdb=" O GLU A 696 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU A 703 " --> pdb=" O GLN A 699 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN A 705 " --> pdb=" O MET A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 721 removed outlier: 3.911A pdb=" N THR A 717 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU A 721 " --> pdb=" O THR A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 726 removed outlier: 3.540A pdb=" N LYS A 726 " --> pdb=" O ALA A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 754 removed outlier: 4.653A pdb=" N LYS A 733 " --> pdb=" O GLU A 729 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 751 " --> pdb=" O ASP A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 767 removed outlier: 5.461A pdb=" N ARG A 763 " --> pdb=" O MET A 760 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ASN A 764 " --> pdb=" O MET A 761 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASP A 767 " --> pdb=" O ASN A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 780 removed outlier: 3.552A pdb=" N GLY A 775 " --> pdb=" O LYS A 771 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A 776 " --> pdb=" O LEU A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 792 removed outlier: 3.607A pdb=" N SER A 789 " --> pdb=" O TYR A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 827 removed outlier: 3.697A pdb=" N ASP A 800 " --> pdb=" O THR A 796 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN A 805 " --> pdb=" O GLY A 801 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA A 811 " --> pdb=" O LYS A 807 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU A 812 " --> pdb=" O GLU A 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 84 removed outlier: 3.776A pdb=" N ALA C 82 " --> pdb=" O LEU C 78 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TYR C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 81 removed outlier: 4.029A pdb=" N LEU D 81 " --> pdb=" O LEU D 78 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 110 through 113 removed outlier: 4.996A pdb=" N PHE B 111 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU B 94 " --> pdb=" O PHE B 111 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER B 93 " --> pdb=" O MET B 191 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE B 180 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL B 189 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR B 178 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N MET B 191 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N LEU B 176 " --> pdb=" O MET B 191 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 175 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL B 151 " --> pdb=" O ILE B 175 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 98 through 100 Processing sheet with id=AA3, first strand: chain 'B' and resid 328 through 330 removed outlier: 3.695A pdb=" N LYS B 328 " --> pdb=" O ASP B 318 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS B 315 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL B 396 " --> pdb=" O LEU B 278 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE B 388 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL B 398 " --> pdb=" O MET B 386 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N MET B 386 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR B 400 " --> pdb=" O LEU B 384 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU B 384 " --> pdb=" O THR B 400 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 133 through 134 removed outlier: 6.542A pdb=" N LEU A 96 " --> pdb=" O ARG A 111 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N PHE A 113 " --> pdb=" O MET A 94 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N MET A 94 " --> pdb=" O PHE A 113 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL A 115 " --> pdb=" O ASP A 92 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ASP A 92 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ARG A 93 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL A 195 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL A 189 " --> pdb=" O TYR A 99 " (cutoff:3.500A) removed outlier: 11.631A pdb=" N ALA A 101 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 14.548A pdb=" N ASP A 187 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ILE A 182 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ILE A 191 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N SER A 180 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N MET A 193 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU A 178 " --> pdb=" O MET A 193 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 328 through 333 removed outlier: 3.641A pdb=" N VAL A 318 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS A 317 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL A 398 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE A 390 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N VAL A 400 " --> pdb=" O MET A 388 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N MET A 388 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N THR A 402 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU A 386 " --> pdb=" O THR A 402 " (cutoff:3.500A) 621 hydrogen bonds defined for protein. 1761 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.00 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 13809 1.02 - 1.22: 31 1.22 - 1.42: 6045 1.42 - 1.62: 8176 1.62 - 1.82: 162 Bond restraints: 28223 Sorted by residual: bond pdb=" O2P 35G A 903 " pdb=" P 35G A 903 " ideal model delta sigma weight residual 1.587 1.469 0.118 2.00e-02 2.50e+03 3.46e+01 bond pdb=" O1P 35G A 903 " pdb=" P 35G A 903 " ideal model delta sigma weight residual 1.462 1.562 -0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" N MET A 798 " pdb=" CA MET A 798 " ideal model delta sigma weight residual 1.459 1.413 0.046 1.28e-02 6.10e+03 1.30e+01 bond pdb=" C MET A 798 " pdb=" O MET A 798 " ideal model delta sigma weight residual 1.236 1.196 0.040 1.26e-02 6.30e+03 1.01e+01 bond pdb=" CA MET A 798 " pdb=" CB MET A 798 " ideal model delta sigma weight residual 1.528 1.481 0.047 1.66e-02 3.63e+03 8.03e+00 ... (remaining 28218 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.81: 51023 8.81 - 17.63: 0 17.63 - 26.44: 1 26.44 - 35.25: 2 35.25 - 44.06: 3 Bond angle restraints: 51029 Sorted by residual: angle pdb=" O1P 35G B 903 " pdb=" P 35G B 903 " pdb=" O5' 35G B 903 " ideal model delta sigma weight residual 113.89 69.83 44.06 3.00e+00 1.11e-01 2.16e+02 angle pdb=" O1P 35G A 903 " pdb=" P 35G A 903 " pdb=" O2P 35G A 903 " ideal model delta sigma weight residual 116.51 80.79 35.72 3.00e+00 1.11e-01 1.42e+02 angle pdb=" O1P 35G B 903 " pdb=" P 35G B 903 " pdb=" O2P 35G B 903 " ideal model delta sigma weight residual 116.51 80.85 35.66 3.00e+00 1.11e-01 1.41e+02 angle pdb=" O2P 35G B 903 " pdb=" P 35G B 903 " pdb=" O5' 35G B 903 " ideal model delta sigma weight residual 101.38 134.85 -33.47 3.00e+00 1.11e-01 1.24e+02 angle pdb=" O2P 35G A 903 " pdb=" P 35G A 903 " pdb=" O5' 35G A 903 " ideal model delta sigma weight residual 101.38 68.89 32.49 3.00e+00 1.11e-01 1.17e+02 ... (remaining 51024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.56: 12574 26.56 - 53.12: 640 53.12 - 79.68: 68 79.68 - 106.24: 11 106.24 - 132.80: 2 Dihedral angle restraints: 13295 sinusoidal: 7217 harmonic: 6078 Sorted by residual: dihedral pdb=" CB CYS B 84 " pdb=" SG CYS B 84 " pdb=" SG CYS B 92 " pdb=" CB CYS B 92 " ideal model delta sinusoidal sigma weight residual -86.00 -175.31 89.31 1 1.00e+01 1.00e-02 9.49e+01 dihedral pdb=" CA HIS C 75 " pdb=" C HIS C 75 " pdb=" N LEU C 76 " pdb=" CA LEU C 76 " ideal model delta harmonic sigma weight residual 180.00 157.00 23.00 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" C5' 35G B 903 " pdb=" O5' 35G B 903 " pdb=" P 35G B 903 " pdb=" O2P 35G B 903 " ideal model delta sinusoidal sigma weight residual 68.89 -158.31 -132.80 1 3.00e+01 1.11e-03 1.79e+01 ... (remaining 13292 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.471: 2120 0.471 - 0.942: 0 0.942 - 1.413: 0 1.413 - 1.883: 0 1.883 - 2.354: 1 Chirality restraints: 2121 Sorted by residual: chirality pdb=" P 35G B 903 " pdb=" O2P 35G B 903 " pdb=" O3' 35G B 903 " pdb=" O5' 35G B 903 " both_signs ideal model delta sigma weight residual True 3.56 1.21 2.35 2.00e-01 2.50e+01 1.39e+02 chirality pdb=" P 35G A 903 " pdb=" O2P 35G A 903 " pdb=" O3' 35G A 903 " pdb=" O5' 35G A 903 " both_signs ideal model delta sigma weight residual True 3.56 3.23 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CA THR A 796 " pdb=" N THR A 796 " pdb=" C THR A 796 " pdb=" CB THR A 796 " both_signs ideal model delta sigma weight residual False 2.53 2.21 0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 2118 not shown) Planarity restraints: 4151 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 35G A 903 " 0.062 2.00e-02 2.50e+03 2.56e-02 1.97e+01 pdb=" C2 35G A 903 " -0.003 2.00e-02 2.50e+03 pdb=" C4 35G A 903 " -0.010 2.00e-02 2.50e+03 pdb=" C5 35G A 903 " -0.009 2.00e-02 2.50e+03 pdb=" C6 35G A 903 " 0.011 2.00e-02 2.50e+03 pdb=" C8 35G A 903 " -0.030 2.00e-02 2.50e+03 pdb=" N1 35G A 903 " 0.012 2.00e-02 2.50e+03 pdb=" N2 35G A 903 " -0.023 2.00e-02 2.50e+03 pdb=" N3 35G A 903 " -0.010 2.00e-02 2.50e+03 pdb=" N7 35G A 903 " -0.025 2.00e-02 2.50e+03 pdb=" N9 35G A 903 " -0.013 2.00e-02 2.50e+03 pdb=" O6 35G A 903 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 798 " -0.019 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" N LEU A 799 " 0.061 2.00e-02 2.50e+03 pdb=" CA LEU A 799 " -0.015 2.00e-02 2.50e+03 pdb=" H LEU A 799 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 27 " -0.056 5.00e-02 4.00e+02 8.36e-02 1.12e+01 pdb=" N PRO C 28 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO C 28 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 28 " -0.046 5.00e-02 4.00e+02 ... (remaining 4148 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 878 2.15 - 2.76: 52078 2.76 - 3.37: 77531 3.37 - 3.99: 97482 3.99 - 4.60: 156089 Nonbonded interactions: 384058 Sorted by model distance: nonbonded pdb=" HG1 THR A 693 " pdb=" OE1 GLN A 694 " model vdw 1.533 2.450 nonbonded pdb=" HE1 TRP B 290 " pdb=" OE2 GLU A 709 " model vdw 1.567 2.450 nonbonded pdb=" O VAL A 685 " pdb=" HG SER A 688 " model vdw 1.576 2.450 nonbonded pdb=" O GLY A 801 " pdb="HD22 ASN A 805 " model vdw 1.583 2.450 nonbonded pdb=" OD1 ASN A 645 " pdb=" H PHE A 647 " model vdw 1.595 2.450 ... (remaining 384053 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 10 through 39 or resid 72 through 87)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 34.320 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.118 14389 Z= 0.141 Angle : 0.814 44.065 19450 Z= 0.355 Chirality : 0.064 2.354 2121 Planarity : 0.004 0.084 2504 Dihedral : 14.944 132.796 5447 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 0.13 % Allowed : 0.33 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.21), residues: 1712 helix: 0.66 (0.20), residues: 821 sheet: -0.86 (0.48), residues: 129 loop : -1.35 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 15 TYR 0.009 0.001 TYR B 454 PHE 0.014 0.001 PHE A 788 TRP 0.028 0.001 TRP A 697 HIS 0.004 0.001 HIS A 792 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (14384) covalent geometry : angle 0.81295 / 0.35 (19448) SS BOND : bond 0.00011 / 0.01 ( 1) SS BOND : angle 3.43633 / 1.88 ( 2) hydrogen bonds : bond 0.20003 / 12.99 ( 621) hydrogen bonds : angle 6.89772 / 4.69 ( 1761) metal coordination : bond 0.00082 / 0.04 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 9 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Evaluate side-chains 546 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 544 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 273 TYR cc_start: 0.8617 (p90) cc_final: 0.8295 (p90) REVERT: A 86 CYS cc_start: 0.5899 (m) cc_final: 0.5588 (m) REVERT: A 180 SER cc_start: 0.8096 (t) cc_final: 0.7735 (p) REVERT: A 550 SER cc_start: 0.8364 (t) cc_final: 0.8116 (p) REVERT: A 798 MET cc_start: 0.6570 (OUTLIER) cc_final: 0.6288 (ttp) outliers start: 2 outliers final: 0 residues processed: 544 average time/residue: 0.2844 time to fit residues: 218.9831 Evaluate side-chains 365 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 364 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 798 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.0270 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 522 GLN A 361 ASN A 608 ASN A 804 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.083323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.074318 restraints weight = 94062.792| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.69 r_work: 0.3027 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14389 Z= 0.166 Angle : 0.760 34.061 19450 Z= 0.360 Chirality : 0.060 2.017 2121 Planarity : 0.005 0.057 2504 Dihedral : 7.193 112.277 1928 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.68 % Favored : 94.21 % Rotamer: Outliers : 1.30 % Allowed : 12.17 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.21), residues: 1712 helix: 0.77 (0.19), residues: 837 sheet: -0.75 (0.46), residues: 141 loop : -1.49 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 48 TYR 0.012 0.001 TYR A 404 PHE 0.016 0.001 PHE B 215 TRP 0.009 0.001 TRP A 697 HIS 0.007 0.001 HIS A 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (14384) covalent geometry : angle 0.75991 / 0.36 (19448) SS BOND : bond 0.00225 / 0.12 ( 1) SS BOND : angle 1.41328 / 0.77 ( 2) hydrogen bonds : bond 0.05603 / 3.73 ( 621) hydrogen bonds : angle 5.40899 / 3.75 ( 1761) metal coordination : bond 0.00202 / 0.10 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 9 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Evaluate side-chains 388 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 368 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 442 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7494 (tm-30) REVERT: B 487 LYS cc_start: 0.8978 (mttp) cc_final: 0.8701 (tptp) REVERT: B 515 GLU cc_start: 0.8682 (mp0) cc_final: 0.8262 (mp0) REVERT: A 108 LEU cc_start: 0.8780 (mt) cc_final: 0.8508 (mp) REVERT: A 180 SER cc_start: 0.9291 (t) cc_final: 0.8890 (p) REVERT: A 444 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7947 (tm-30) REVERT: A 550 SER cc_start: 0.9360 (t) cc_final: 0.9124 (p) REVERT: D 32 GLN cc_start: 0.7484 (pp30) cc_final: 0.7158 (pp30) outliers start: 20 outliers final: 16 residues processed: 374 average time/residue: 0.2782 time to fit residues: 150.0059 Evaluate side-chains 369 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 353 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 350 GLU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 511 CYS Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 804 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 126 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.083006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.073941 restraints weight = 93714.190| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.69 r_work: 0.3017 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14389 Z= 0.136 Angle : 0.733 33.668 19450 Z= 0.341 Chirality : 0.059 2.002 2121 Planarity : 0.004 0.064 2504 Dihedral : 6.976 108.085 1925 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.62 % Favored : 94.27 % Rotamer: Outliers : 1.24 % Allowed : 14.12 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.21), residues: 1712 helix: 0.75 (0.19), residues: 853 sheet: -0.63 (0.47), residues: 141 loop : -1.62 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 48 TYR 0.011 0.001 TYR A 583 PHE 0.012 0.001 PHE B 215 TRP 0.013 0.001 TRP A 697 HIS 0.011 0.001 HIS A 599 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (14384) covalent geometry : angle 0.73266 / 0.34 (19448) SS BOND : bond 0.00165 / 0.09 ( 1) SS BOND : angle 1.17479 / 0.62 ( 2) hydrogen bonds : bond 0.04672 / 3.12 ( 621) hydrogen bonds : angle 5.10162 / 3.55 ( 1761) metal coordination : bond 0.00120 / 0.06 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 9 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Evaluate side-chains 379 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 360 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8487 (tm-30) REVERT: B 215 PHE cc_start: 0.8172 (p90) cc_final: 0.7735 (p90) REVERT: B 358 MET cc_start: 0.8814 (mmm) cc_final: 0.8516 (tpp) REVERT: B 462 GLU cc_start: 0.8435 (pt0) cc_final: 0.8013 (pt0) REVERT: B 481 GLU cc_start: 0.7545 (tp30) cc_final: 0.7296 (tp30) REVERT: B 515 GLU cc_start: 0.8752 (mp0) cc_final: 0.8447 (mp0) REVERT: B 584 ASP cc_start: 0.8288 (t0) cc_final: 0.8013 (t0) REVERT: A 180 SER cc_start: 0.9292 (t) cc_final: 0.8898 (p) REVERT: A 444 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7965 (tm-30) REVERT: A 550 SER cc_start: 0.9334 (t) cc_final: 0.9109 (p) REVERT: D 32 GLN cc_start: 0.7591 (pp30) cc_final: 0.7386 (pp30) outliers start: 19 outliers final: 12 residues processed: 367 average time/residue: 0.2791 time to fit residues: 147.6473 Evaluate side-chains 359 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 347 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 511 CYS Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 804 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 124 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 73 optimal weight: 0.0980 chunk 0 optimal weight: 5.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 34 ASN B 67 GLN ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN A 361 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.079220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.070411 restraints weight = 95321.294| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.61 r_work: 0.2945 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2815 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2815 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 14389 Z= 0.257 Angle : 0.782 35.174 19450 Z= 0.376 Chirality : 0.059 1.927 2121 Planarity : 0.005 0.076 2504 Dihedral : 7.066 115.627 1925 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.90 % Favored : 92.98 % Rotamer: Outliers : 1.63 % Allowed : 15.48 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.20), residues: 1712 helix: 0.60 (0.18), residues: 859 sheet: -0.72 (0.46), residues: 141 loop : -1.79 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 48 TYR 0.015 0.002 TYR B 273 PHE 0.016 0.002 PHE B 632 TRP 0.015 0.001 TRP A 697 HIS 0.006 0.001 HIS B 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.26 (14384) covalent geometry : angle 0.78171 / 0.38 (19448) SS BOND : bond 0.00229 / 0.12 ( 1) SS BOND : angle 1.10644 / 0.58 ( 2) hydrogen bonds : bond 0.04673 / 3.12 ( 621) hydrogen bonds : angle 5.13734 / 3.59 ( 1761) metal coordination : bond 0.00489 / 0.25 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 9 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Evaluate side-chains 376 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 351 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 326 ASP cc_start: 0.8511 (t0) cc_final: 0.8295 (t0) REVERT: B 510 GLU cc_start: 0.8256 (mt-10) cc_final: 0.8047 (mt-10) REVERT: B 537 GLN cc_start: 0.8108 (mp10) cc_final: 0.7747 (mp10) REVERT: B 584 ASP cc_start: 0.8311 (t0) cc_final: 0.8046 (t0) REVERT: A 70 ASP cc_start: 0.7957 (t0) cc_final: 0.7731 (t70) REVERT: A 180 SER cc_start: 0.9263 (t) cc_final: 0.8872 (p) REVERT: A 550 SER cc_start: 0.9322 (t) cc_final: 0.9110 (p) REVERT: A 697 TRP cc_start: 0.8746 (t-100) cc_final: 0.8452 (t-100) REVERT: D 32 GLN cc_start: 0.7461 (pp30) cc_final: 0.7174 (pp30) REVERT: D 78 LEU cc_start: 0.8125 (tt) cc_final: 0.7919 (tp) outliers start: 25 outliers final: 19 residues processed: 362 average time/residue: 0.2709 time to fit residues: 141.6911 Evaluate side-chains 360 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 341 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 479 ASP Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain D residue 22 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 137 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN A 384 ASN C 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.085682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.075849 restraints weight = 98556.356| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.76 r_work: 0.3022 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14389 Z= 0.204 Angle : 0.755 34.815 19450 Z= 0.359 Chirality : 0.059 1.959 2121 Planarity : 0.004 0.061 2504 Dihedral : 7.080 112.806 1925 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.55 % Favored : 93.33 % Rotamer: Outliers : 1.63 % Allowed : 15.74 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.20), residues: 1712 helix: 0.64 (0.18), residues: 860 sheet: -0.87 (0.45), residues: 143 loop : -1.78 (0.22), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 48 TYR 0.014 0.001 TYR B 273 PHE 0.014 0.001 PHE A 565 TRP 0.015 0.001 TRP A 697 HIS 0.005 0.001 HIS A 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.20 (14384) covalent geometry : angle 0.75507 / 0.36 (19448) SS BOND : bond 0.00218 / 0.11 ( 1) SS BOND : angle 0.88679 / 0.47 ( 2) hydrogen bonds : bond 0.04451 / 2.97 ( 621) hydrogen bonds : angle 5.00659 / 3.49 ( 1761) metal coordination : bond 0.00300 / 0.15 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 9 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Evaluate side-chains 374 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 349 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 326 ASP cc_start: 0.8516 (t0) cc_final: 0.8256 (t0) REVERT: B 417 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8438 (tp) REVERT: B 584 ASP cc_start: 0.8255 (t0) cc_final: 0.8047 (t0) REVERT: A 70 ASP cc_start: 0.7993 (t0) cc_final: 0.7719 (t70) REVERT: A 180 SER cc_start: 0.9224 (t) cc_final: 0.8831 (p) REVERT: A 242 LEU cc_start: 0.9284 (tp) cc_final: 0.9066 (tp) REVERT: A 550 SER cc_start: 0.9307 (t) cc_final: 0.9097 (p) REVERT: D 32 GLN cc_start: 0.7514 (pp30) cc_final: 0.7234 (pp30) outliers start: 25 outliers final: 21 residues processed: 364 average time/residue: 0.2666 time to fit residues: 140.6632 Evaluate side-chains 366 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 344 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 479 ASP Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 511 CYS Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain D residue 22 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 78 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 123 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 69 ASN ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.086299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.076418 restraints weight = 98238.201| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.79 r_work: 0.3033 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14389 Z= 0.158 Angle : 0.738 34.389 19450 Z= 0.345 Chirality : 0.059 1.974 2121 Planarity : 0.005 0.086 2504 Dihedral : 6.999 111.846 1925 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.26 % Favored : 93.62 % Rotamer: Outliers : 1.69 % Allowed : 16.59 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.21), residues: 1712 helix: 0.82 (0.19), residues: 859 sheet: -0.88 (0.45), residues: 143 loop : -1.73 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 48 TYR 0.013 0.001 TYR B 273 PHE 0.016 0.001 PHE B 287 TRP 0.014 0.001 TRP A 697 HIS 0.006 0.001 HIS D 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (14384) covalent geometry : angle 0.73841 / 0.35 (19448) SS BOND : bond 0.00250 / 0.13 ( 1) SS BOND : angle 0.77965 / 0.41 ( 2) hydrogen bonds : bond 0.04106 / 2.74 ( 621) hydrogen bonds : angle 4.83329 / 3.36 ( 1761) metal coordination : bond 0.00213 / 0.11 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 9 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Evaluate side-chains 371 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 345 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 129 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8059 (mm-30) REVERT: B 326 ASP cc_start: 0.8559 (t0) cc_final: 0.8276 (t0) REVERT: B 417 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8415 (tp) REVERT: B 502 TYR cc_start: 0.8034 (m-10) cc_final: 0.6892 (m-10) REVERT: B 526 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8346 (mt-10) REVERT: B 537 GLN cc_start: 0.8145 (mp10) cc_final: 0.7852 (mp10) REVERT: A 70 ASP cc_start: 0.8011 (t0) cc_final: 0.7749 (t70) REVERT: A 180 SER cc_start: 0.9234 (t) cc_final: 0.8853 (p) REVERT: A 242 LEU cc_start: 0.9289 (tp) cc_final: 0.9070 (tp) REVERT: A 421 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8676 (tm-30) REVERT: A 550 SER cc_start: 0.9283 (t) cc_final: 0.9062 (p) REVERT: A 814 ASP cc_start: 0.8540 (m-30) cc_final: 0.8060 (p0) REVERT: D 32 GLN cc_start: 0.7552 (pp30) cc_final: 0.7299 (pp30) outliers start: 26 outliers final: 23 residues processed: 359 average time/residue: 0.2747 time to fit residues: 142.5068 Evaluate side-chains 362 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 338 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 479 ASP Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 639 GLU Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 94 MET Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 661 MET Chi-restraints excluded: chain A residue 686 ASP Chi-restraints excluded: chain D residue 22 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 93 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 162 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 52 GLN ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.086346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.076541 restraints weight = 97559.573| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.76 r_work: 0.3036 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2902 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14389 Z= 0.151 Angle : 0.737 34.465 19450 Z= 0.344 Chirality : 0.058 1.958 2121 Planarity : 0.004 0.062 2504 Dihedral : 6.933 114.452 1925 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.50 % Favored : 93.39 % Rotamer: Outliers : 1.56 % Allowed : 16.98 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.21), residues: 1712 helix: 0.95 (0.19), residues: 857 sheet: -0.86 (0.45), residues: 143 loop : -1.68 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 48 TYR 0.012 0.001 TYR B 273 PHE 0.011 0.001 PHE B 632 TRP 0.015 0.001 TRP A 697 HIS 0.006 0.001 HIS D 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (14384) covalent geometry : angle 0.73660 / 0.34 (19448) SS BOND : bond 0.00233 / 0.12 ( 1) SS BOND : angle 0.71953 / 0.38 ( 2) hydrogen bonds : bond 0.03958 / 2.65 ( 621) hydrogen bonds : angle 4.75281 / 3.31 ( 1761) metal coordination : bond 0.00204 / 0.10 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 9 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Evaluate side-chains 365 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 341 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 129 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8105 (mm-30) REVERT: B 326 ASP cc_start: 0.8570 (t0) cc_final: 0.8274 (t0) REVERT: B 417 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8413 (tp) REVERT: B 459 ASP cc_start: 0.8211 (p0) cc_final: 0.8009 (p0) REVERT: B 812 ASP cc_start: 0.8717 (t0) cc_final: 0.8297 (t0) REVERT: B 815 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7722 (tm-30) REVERT: A 70 ASP cc_start: 0.8032 (t0) cc_final: 0.7784 (t70) REVERT: A 180 SER cc_start: 0.9235 (t) cc_final: 0.8860 (p) REVERT: A 242 LEU cc_start: 0.9296 (tp) cc_final: 0.9080 (tp) REVERT: A 421 GLU cc_start: 0.8855 (tm-30) cc_final: 0.8644 (tm-30) REVERT: A 483 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7851 (mt-10) REVERT: A 550 SER cc_start: 0.9283 (t) cc_final: 0.9057 (p) REVERT: A 814 ASP cc_start: 0.8567 (m-30) cc_final: 0.8081 (p0) REVERT: D 32 GLN cc_start: 0.7539 (pp30) cc_final: 0.7330 (pp30) outliers start: 24 outliers final: 18 residues processed: 353 average time/residue: 0.2800 time to fit residues: 142.3638 Evaluate side-chains 356 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 337 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 479 ASP Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain A residue 157 GLU Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain D residue 22 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 166 optimal weight: 5.9990 chunk 146 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.085691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.075918 restraints weight = 98259.648| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.76 r_work: 0.3026 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14389 Z= 0.172 Angle : 0.748 34.767 19450 Z= 0.351 Chirality : 0.058 1.939 2121 Planarity : 0.004 0.062 2504 Dihedral : 6.907 118.568 1925 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.96 % Favored : 92.92 % Rotamer: Outliers : 1.95 % Allowed : 16.79 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.21), residues: 1712 helix: 0.98 (0.19), residues: 856 sheet: -0.93 (0.45), residues: 143 loop : -1.73 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 48 TYR 0.012 0.001 TYR B 273 PHE 0.013 0.001 PHE B 632 TRP 0.014 0.001 TRP A 697 HIS 0.007 0.001 HIS D 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (14384) covalent geometry : angle 0.74823 / 0.35 (19448) SS BOND : bond 0.00233 / 0.12 ( 1) SS BOND : angle 0.72267 / 0.38 ( 2) hydrogen bonds : bond 0.03980 / 2.65 ( 621) hydrogen bonds : angle 4.73583 / 3.30 ( 1761) metal coordination : bond 0.00244 / 0.12 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 9 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Evaluate side-chains 370 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 340 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 326 ASP cc_start: 0.8588 (t0) cc_final: 0.8300 (t0) REVERT: B 417 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8421 (tp) REVERT: B 526 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8368 (mt-10) REVERT: B 815 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7754 (tm-30) REVERT: A 70 ASP cc_start: 0.8111 (t0) cc_final: 0.7894 (t70) REVERT: A 180 SER cc_start: 0.9271 (t) cc_final: 0.8870 (p) REVERT: A 242 LEU cc_start: 0.9305 (tp) cc_final: 0.9089 (tp) REVERT: A 550 SER cc_start: 0.9289 (t) cc_final: 0.9071 (p) outliers start: 30 outliers final: 24 residues processed: 357 average time/residue: 0.2760 time to fit residues: 142.5018 Evaluate side-chains 359 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 334 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 479 ASP Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 598 ASP Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 665 ILE Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 686 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain D residue 22 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 164 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 151 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.086925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.077136 restraints weight = 97398.005| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.76 r_work: 0.3055 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14389 Z= 0.119 Angle : 0.733 34.111 19450 Z= 0.339 Chirality : 0.058 1.954 2121 Planarity : 0.004 0.062 2504 Dihedral : 6.805 119.555 1925 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.20 % Favored : 93.68 % Rotamer: Outliers : 1.37 % Allowed : 17.89 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.21), residues: 1712 helix: 1.12 (0.19), residues: 850 sheet: -0.85 (0.45), residues: 143 loop : -1.66 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 48 TYR 0.011 0.001 TYR B 273 PHE 0.011 0.001 PHE B 287 TRP 0.012 0.001 TRP A 697 HIS 0.006 0.001 HIS D 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (14384) covalent geometry : angle 0.73277 / 0.34 (19448) SS BOND : bond 0.00233 / 0.12 ( 1) SS BOND : angle 0.62186 / 0.33 ( 2) hydrogen bonds : bond 0.03696 / 2.46 ( 621) hydrogen bonds : angle 4.58924 / 3.20 ( 1761) metal coordination : bond 0.00117 / 0.06 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 9 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Evaluate side-chains 359 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 338 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 326 ASP cc_start: 0.8584 (t0) cc_final: 0.8290 (t0) REVERT: B 358 MET cc_start: 0.8607 (mmm) cc_final: 0.8232 (tpt) REVERT: B 417 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8375 (tp) REVERT: B 526 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8364 (mt-10) REVERT: B 815 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7692 (tm-30) REVERT: A 70 ASP cc_start: 0.8077 (t0) cc_final: 0.7836 (t70) REVERT: A 180 SER cc_start: 0.9233 (t) cc_final: 0.8851 (p) REVERT: A 550 SER cc_start: 0.9280 (t) cc_final: 0.9054 (p) REVERT: A 814 ASP cc_start: 0.8556 (m-30) cc_final: 0.8068 (p0) outliers start: 21 outliers final: 17 residues processed: 347 average time/residue: 0.2881 time to fit residues: 144.0166 Evaluate side-chains 352 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 334 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 479 ASP Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 665 ILE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 686 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 147 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 10 optimal weight: 0.0170 chunk 61 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 overall best weight: 1.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.086628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.076895 restraints weight = 97138.637| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.73 r_work: 0.3052 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14389 Z= 0.134 Angle : 0.740 34.310 19450 Z= 0.344 Chirality : 0.057 1.934 2121 Planarity : 0.004 0.062 2504 Dihedral : 6.742 124.690 1925 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.55 % Favored : 93.33 % Rotamer: Outliers : 1.37 % Allowed : 17.96 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.21), residues: 1712 helix: 1.15 (0.19), residues: 849 sheet: -0.80 (0.45), residues: 143 loop : -1.64 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 48 TYR 0.011 0.001 TYR A 404 PHE 0.010 0.001 PHE A 565 TRP 0.011 0.001 TRP A 697 HIS 0.006 0.001 HIS D 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (14384) covalent geometry : angle 0.74015 / 0.34 (19448) SS BOND : bond 0.00236 / 0.12 ( 1) SS BOND : angle 0.63582 / 0.34 ( 2) hydrogen bonds : bond 0.03640 / 2.42 ( 621) hydrogen bonds : angle 4.56274 / 3.18 ( 1761) metal coordination : bond 0.00176 / 0.09 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 9 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Evaluate side-chains 359 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 338 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 326 ASP cc_start: 0.8591 (t0) cc_final: 0.8303 (t0) REVERT: B 358 MET cc_start: 0.8642 (mmm) cc_final: 0.8255 (tpt) REVERT: B 417 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8399 (tp) REVERT: B 491 GLU cc_start: 0.8335 (tt0) cc_final: 0.8078 (tt0) REVERT: B 526 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8373 (mt-10) REVERT: B 815 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7658 (tm-30) REVERT: A 70 ASP cc_start: 0.8109 (t0) cc_final: 0.7876 (t70) REVERT: A 180 SER cc_start: 0.9212 (t) cc_final: 0.8842 (p) REVERT: A 550 SER cc_start: 0.9286 (t) cc_final: 0.9064 (p) REVERT: A 814 ASP cc_start: 0.8564 (m-30) cc_final: 0.8077 (p0) outliers start: 21 outliers final: 18 residues processed: 349 average time/residue: 0.2714 time to fit residues: 136.7526 Evaluate side-chains 356 residues out of total 1543 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 337 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 201 PHE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 479 ASP Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 665 ILE Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 686 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 12 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 128 optimal weight: 0.3980 chunk 121 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 113 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 112 optimal weight: 0.0980 chunk 80 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.088195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.078508 restraints weight = 96715.917| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.73 r_work: 0.3081 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (4 function evaluations) r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14389 Z= 0.111 Angle : 0.732 33.691 19450 Z= 0.336 Chirality : 0.057 1.942 2121 Planarity : 0.004 0.062 2504 Dihedral : 6.640 129.038 1925 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.85 % Favored : 94.03 % Rotamer: Outliers : 1.11 % Allowed : 18.15 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.21), residues: 1712 helix: 1.30 (0.19), residues: 843 sheet: -0.68 (0.45), residues: 143 loop : -1.58 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 48 TYR 0.009 0.001 TYR B 273 PHE 0.010 0.001 PHE B 215 TRP 0.011 0.001 TRP A 480 HIS 0.006 0.001 HIS D 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (14384) covalent geometry : angle 0.73167 / 0.34 (19448) SS BOND : bond 0.00233 / 0.12 ( 1) SS BOND : angle 0.55952 / 0.30 ( 2) hydrogen bonds : bond 0.03385 / 2.25 ( 621) hydrogen bonds : angle 4.43454 / 3.09 ( 1761) metal coordination : bond 0.00082 / 0.04 ( 4) =============================================================================== Job complete usr+sys time: 7367.16 seconds wall clock time: 125 minutes 21.35 seconds (7521.35 seconds total)